Primary alignment filtering

[HJeffery]

Hi,

I've found a way to reduce background repeat counts.

In line 333 of https://github.com/unique379r/strspy/blob/main/scripts/STRspy_v1.0.sh reads are filtered so that only unmapped are eliminated from repeat counting.

If swapped to keep only primary alignments (-F 2308) instead of -F 4 which also keeps secondary and supplementary alignments, this leads to much tidier repeat counting and reduced background repeat counts.

I propose changing filtering from -F 4 to -F 2308.

Thank you.

[fritzsedlazeck]

Thanks Heather thats a great suggestion!

[HJeffery]

Thanks Fritz!